Dynamic::~Dynamic()
{
INFO ("Dynamic seeeding required " + str (total_samples) + " samples to draw " + str (total_seeds) + " seeds");
#ifdef DYNAMIC_SEED_DEBUGGING
const double final_mu = mu();
// Output seeding probabilites at end of execution
Image::Header H;
H.info() = info();
H.datatype() = DataType::Float32;
Image::Buffer<float> prob_mean_data ("seed_prob_mean.mif", H), prob_sum_data ("seed_prob_sum.mif", H);
Image::Buffer<float>::voxel_type prob_mean (prob_mean_data), prob_sum (prob_sum_data);
VoxelAccessor v (accessor);
Image::Loop loop;
for (loop.start (v, prob_mean, prob_sum); loop.ok(); loop.next (v, prob_mean, prob_sum)) {
if (v.value()) {
float sum = 0.0;
size_t count = 0;
for (Fixel_map<Fixel_TD_seed>::ConstIterator i = begin (v); i; ++i) {
sum += i().get_seed_prob (final_mu);
++count;
}
prob_mean.value() = sum / float(count);
prob_sum .value() = sum;
}
}
#endif
}
bool Dynamic::operator() (const FMLS::FOD_lobes& in)
{
if (!SIFT::ModelBase<Fixel_TD_seed>::operator() (in))
return false;
VoxelAccessor v (accessor);
Image::Nav::set_pos (v, in.vox);
if (v.value()) {
for (DWI::Fixel_map<Fixel>::Iterator i = begin (v); i; ++i)
i().set_voxel (in.vox);
}
return true;
}
value_type AFDConnectivity::get (const std::string& path)
{
Tractography::Properties properties;
Tractography::Reader<value_type> reader (path, properties);
const size_t track_count = (properties.find ("count") == properties.end() ? 0 : to<size_t>(properties["count"]));
DWI::Tractography::Mapping::TrackLoader loader (reader, track_count, "summing apparent fibre density within track");
// If WBFT is provided, this is the sum of (volume/length) across streamlines
// Otherwise, it's a sum of lengths of all streamlines (for later scaling by mean streamline length)
double sum_contributions = 0.0;
size_t count = 0;
Tractography::Streamline<value_type> tck;
while (loader (tck)) {
++count;
SetDixel dixels;
mapper (tck, dixels);
double this_length = 0.0, this_volume = 0.0;
for (SetDixel::const_iterator i = dixels.begin(); i != dixels.end(); ++i) {
this_length += i->get_length();
// If wbft has not been provided (i.e. FODs have not been pre-segmented), need to
// check to see if any data have been provided for this voxel; and if not yet,
// run the segmenter
if (!have_wbft) {
VoxelAccessor v (accessor());
assign_pos_of (*i, 0, 3).to (v);
if (!v.value()) {
assign_pos_of (*i, 0, 3).to (v_fod);
DWI::FMLS::SH_coefs fod_data;
DWI::FMLS::FOD_lobes fod_lobes;
fod_data.vox[0] = v_fod.index (0); fod_data.vox[1] = v_fod.index (1); fod_data.vox[2] = v_fod.index (2);
fod_data.resize (v_fod.size (3));
for (auto i = Loop(3) (v_fod); i; ++i)
fod_data[v_fod.index (3)] = v_fod.value();
(*fmls) (fod_data, fod_lobes);
(*this) (fod_lobes);
}
}
const size_t fixel_index = dixel2fixel (*i);
Fixel& fixel = fixels[fixel_index];
fixel.add_to_selection (i->get_length());
if (have_wbft)
this_volume += fixel.get_selected_volume (i->get_length());
}
if (have_wbft)
sum_contributions += (this_volume / this_length);
else
sum_contributions += this_length;
}
if (!have_wbft) {
// Streamlines define a fixel mask; go through and get all the fibre volumes
double sum_volumes = 0.0;
if (all_fixels) {
// All fixels contribute to the result
for (std::vector<Fixel>::const_iterator i = fixels.begin(); i != fixels.end(); ++i) {
if (i->is_selected())
sum_volumes += i->get_FOD();
}
} else {
// Only allow one fixel per voxel to contribute to the result
VoxelAccessor v (accessor());
for (auto l = Loop(v) (v); l; ++l) {
if (v.value()) {
value_type voxel_afd = 0.0, max_td = 0.0;
for (Fixel_map<Fixel>::Iterator i = begin (v); i; ++i) {
if (i().get_selected_length() > max_td) {
max_td = i().get_selected_length();
voxel_afd = i().get_FOD();
}
}
sum_volumes += voxel_afd;
}
}
}
// sum_contributions currently stores sum of streamline lengths;
// turn into a mean length, then combine with volume to get a connectivity value
const double mean_length = sum_contributions / double(count);
sum_contributions = sum_volumes / mean_length;
}
return sum_contributions;
}